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Updated the code to throw expeption when main thread is blocked. (#1795)
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* Updated the code to throw expeption when main thread is blocked

* Review comments: Updated docs and added message to the exception

* Review changes
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@aditya-07
aditya-07 committed Jan 25, 2023
1 parent 66290ca commit 8d409c1
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Showing 13 changed files with 367 additions and 171 deletions.
28 changes: 14 additions & 14 deletions workflow/src/main/java/com/google/android/fhir/workflow/FhirEngineDal.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -20,45 +20,45 @@ import ca.uhn.fhir.rest.gclient.UriClientParam
import com.google.android.fhir.FhirEngine
import com.google.android.fhir.getResourceType
import com.google.android.fhir.search.Search
import kotlinx.coroutines.runBlocking
import org.hl7.fhir.instance.model.api.IBaseResource
import org.hl7.fhir.instance.model.api.IIdType
import org.hl7.fhir.r4.model.Library
import org.hl7.fhir.r4.model.Resource
import org.hl7.fhir.r4.model.ResourceType
import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal

class FhirEngineDal(private val fhirEngine: FhirEngine) : FhirDal {
internal class FhirEngineDal(private val fhirEngine: FhirEngine) : FhirDal {
val libs = mutableMapOf<String, Library>()

override fun read(id: IIdType): IBaseResource = runBlocking {
override fun read(id: IIdType): IBaseResource = runBlockingOrThrowMainThreadException {
val clazz = id.getResourceClass()
fhirEngine.get(getResourceType(clazz), id.idPart)
}

override fun create(resource: IBaseResource): Unit = runBlocking {
override fun create(resource: IBaseResource): Unit = runBlockingOrThrowMainThreadException {
fhirEngine.create(resource as Resource)
}

override fun update(resource: IBaseResource) = runBlocking {
override fun update(resource: IBaseResource) = runBlockingOrThrowMainThreadException {
fhirEngine.update(resource as Resource)
}

override fun delete(id: IIdType) = runBlocking {
override fun delete(id: IIdType) = runBlockingOrThrowMainThreadException {
val clazz = id.getResourceClass()
fhirEngine.delete(getResourceType(clazz), id.idPart)
}

override fun search(resourceType: String): Iterable<IBaseResource> = runBlocking {
val search = Search(type = ResourceType.fromCode(resourceType))
when (resourceType) {
"Library" -> libs.values.plus(fhirEngine.search(search))
else -> fhirEngine.search(search)
}.toMutableList()
}
override fun search(resourceType: String): Iterable<IBaseResource> =
runBlockingOrThrowMainThreadException {
val search = Search(type = ResourceType.fromCode(resourceType))
when (resourceType) {
"Library" -> libs.values.plus(fhirEngine.search(search))
else -> fhirEngine.search(search)
}.toMutableList()
}

override fun searchByUrl(resourceType: String, url: String): Iterable<IBaseResource> =
runBlocking {
runBlockingOrThrowMainThreadException {
val search = Search(type = ResourceType.fromCode(resourceType))
search.filter(UriClientParam("url"), { value = url })

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2 changes: 1 addition & 1 deletion workflow/src/main/java/com/google/android/fhir/workflow/FhirEngineLibraryContentProvider.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ import org.hl7.fhir.r4.model.Library
import org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BaseFhirLibrarySourceProvider
import org.opencds.cqf.cql.evaluator.fhir.adapter.r4.AdapterFactory

class FhirEngineLibraryContentProvider(adapterFactory: AdapterFactory) :
internal class FhirEngineLibraryContentProvider(adapterFactory: AdapterFactory) :
BaseFhirLibrarySourceProvider(adapterFactory) {
val libs = mutableMapOf<String, Library>()

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54 changes: 21 additions & 33 deletions workflow/src/main/java/com/google/android/fhir/workflow/FhirEngineRetrieveProvider.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@ import com.google.android.fhir.search.filter.TokenParamFilterCriterion
import com.google.android.fhir.search.query.XFhirQueryTranslator.applyFilterParam
import java.math.BigDecimal
import java.util.Date
import kotlinx.coroutines.runBlocking
import org.hl7.fhir.r4.model.Coding
import org.hl7.fhir.r4.model.DateTimeType
import org.hl7.fhir.r4.model.Enumerations
Expand All @@ -41,7 +40,7 @@ import org.opencds.cqf.cql.engine.runtime.DateTime
import org.opencds.cqf.cql.engine.runtime.Interval
import org.opencds.cqf.cql.engine.terminology.ValueSetInfo

class FhirEngineRetrieveProvider(private val fhirEngine: FhirEngine) :
internal class FhirEngineRetrieveProvider(private val fhirEngine: FhirEngine) :
TerminologyAwareRetrieveProvider() {
override fun retrieve(
context: String?,
Expand All @@ -56,37 +55,26 @@ class FhirEngineRetrieveProvider(private val fhirEngine: FhirEngine) :
dateLowPath: String?,
dateHighPath: String?,
dateRange: Interval?
): Iterable<Any> {
return runBlocking {
if (dataType == null) {
emptyList()
} else if (contextPath == "id" && contextValue == null) {
emptyList()
} else if (contextPath == "id" && contextValue != null) {
listOfNotNull(
safeGet(fhirEngine, ResourceType.fromCode(dataType), "$contextValue"),
safeGet(fhirEngine, ResourceType.fromCode(dataType), "urn:uuid:$contextValue"),
safeGet(fhirEngine, ResourceType.fromCode(dataType), "urn:oid:$contextValue")
)
} else if (codePath == "id" && codes != null) {
codes.mapNotNull { safeGet(fhirEngine, ResourceType.fromCode(dataType), it.code) }
} else {
val search = Search(ResourceType.fromCode(dataType))

// filter by context
filterByContext(context, contextPath, contextValue, dataType, search)

// filter by code in codes
filterByCode(codePath, codes, search)

// filter by code into valueSet
filterByValueSet(codePath, valueSet, search)

// filter by date in range
filterByDateRange(datePath, dateLowPath, dateHighPath, dateRange, search)

fhirEngine.search(search)
}
): Iterable<Any> = runBlockingOrThrowMainThreadException {
if (dataType == null) {
emptyList()
} else if (contextPath == "id" && contextValue == null) {
emptyList()
} else if (contextPath == "id") {
listOfNotNull(
safeGet(fhirEngine, ResourceType.fromCode(dataType), "$contextValue"),
safeGet(fhirEngine, ResourceType.fromCode(dataType), "urn:uuid:$contextValue"),
safeGet(fhirEngine, ResourceType.fromCode(dataType), "urn:oid:$contextValue")
)
} else if (codePath == "id" && codes != null) {
codes.mapNotNull { safeGet(fhirEngine, ResourceType.fromCode(dataType), it.code) }
} else {
val search = Search(ResourceType.fromCode(dataType))
filterByContext(context, contextPath, contextValue, dataType, search)
filterByCode(codePath, codes, search)
filterByValueSet(codePath, valueSet, search)
filterByDateRange(datePath, dateLowPath, dateHighPath, dateRange, search)
fhirEngine.search(search)
}
}

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98 changes: 49 additions & 49 deletions workflow/src/main/java/com/google/android/fhir/workflow/FhirEngineTerminologyProvider.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ import ca.uhn.fhir.context.FhirContext
import com.google.android.fhir.FhirEngine
import com.google.android.fhir.db.ResourceNotFoundException
import com.google.android.fhir.search.search
import kotlinx.coroutines.runBlocking
import org.hl7.fhir.r4.model.CodeSystem
import org.hl7.fhir.r4.model.Resource
import org.hl7.fhir.r4.model.ResourceType
Expand All @@ -32,7 +31,7 @@ import org.opencds.cqf.cql.engine.terminology.TerminologyProvider
import org.opencds.cqf.cql.engine.terminology.ValueSetInfo
import org.opencds.cqf.cql.evaluator.engine.util.ValueSetUtil

class FhirEngineTerminologyProvider(
internal class FhirEngineTerminologyProvider(
private val fhirContext: FhirContext,
private val fhirEngine: FhirEngine
) : TerminologyProvider {
Expand All @@ -45,6 +44,8 @@ class FhirEngineTerminologyProvider(
override fun `in`(code: Code, valueSet: ValueSetInfo): Boolean {
try {
return expand(valueSet).any { it.code == code.code && it.system == code.system }
} catch (b: BlockingMainThreadException) {
throw b
} catch (e: Exception) {
throw TerminologyProviderException(
"Error performing membership check of Code: $code in ValueSet: ${valueSet.id}",
Expand All @@ -53,63 +54,62 @@ class FhirEngineTerminologyProvider(
}
}

override fun expand(valueSetInfo: ValueSetInfo): MutableIterable<Code> {
try {
val valueSet = resolveValueSet(valueSetInfo)
return ValueSetUtil.getCodesInExpansion(fhirContext, valueSet)
?: ValueSetUtil.getCodesInCompose(fhirContext, valueSet)
} catch (e: Exception) {
throw TerminologyProviderException(
"Error performing expansion of ValueSet: ${valueSetInfo.id}",
e
)
}
}

override fun lookup(code: Code, codeSystem: CodeSystemInfo): Code {
try {
val codeSystems = runBlocking {
fhirEngine.search<CodeSystem> {
filter(CodeSystem.CODE, { value = of(code.code) })
filter(CodeSystem.SYSTEM, { value = codeSystem.id })
override fun expand(valueSetInfo: ValueSetInfo): MutableIterable<Code> =
runBlockingOrThrowMainThreadException {
try {
resolveValueSet(valueSetInfo).let {
ValueSetUtil.getCodesInExpansion(fhirContext, it)
?: ValueSetUtil.getCodesInCompose(fhirContext, it)
}
} catch (e: Exception) {
throw TerminologyProviderException(
"Error performing expansion of ValueSet: ${valueSetInfo.id}",
e
)
}
}

val concept = codeSystems.first().concept.first { it.code == code.code }

return Code().apply {
this.code = code.code
display = concept.display
system = codeSystem.id
override fun lookup(code: Code, codeSystem: CodeSystemInfo): Code =
runBlockingOrThrowMainThreadException {
try {
fhirEngine
.search<CodeSystem> {
filter(CodeSystem.CODE, { value = of(code.code) })
filter(CodeSystem.SYSTEM, { value = codeSystem.id })
}
.first()
.concept
.first { it.code == code.code }
.let {
Code().apply {
this.code = code.code
display = it.display
system = codeSystem.id
}
}
} catch (e: Exception) {
throw TerminologyProviderException(
"Error performing lookup of Code: $code in CodeSystem: ${codeSystem.id}",
e
)
}
} catch (e: Exception) {
throw TerminologyProviderException(
"Error performing lookup of Code: $code in CodeSystem: ${codeSystem.id}",
e
)
}
}

private fun searchByUrl(url: String?): List<ValueSet> {
private suspend fun searchByUrl(url: String?): List<ValueSet> {
if (url == null) return emptyList()
return runBlocking { fhirEngine.search { filter(ValueSet.URL, { value = url }) } }
return fhirEngine.search { filter(ValueSet.URL, { value = url }) }
}

private fun searchByIdentifier(identifier: String?): List<ValueSet> {
private suspend fun searchByIdentifier(identifier: String?): List<ValueSet> {
if (identifier == null) return emptyList()
return runBlocking {
fhirEngine.search { filter(ValueSet.IDENTIFIER, { value = of(identifier) }) }
}
return fhirEngine.search { filter(ValueSet.IDENTIFIER, { value = of(identifier) }) }
}

private fun searchById(id: String): List<ValueSet> {
return runBlocking {
listOfNotNull(
safeGet(fhirEngine, ResourceType.ValueSet, id.removePrefix(URN_OID).removePrefix(URN_UUID))
as? ValueSet
)
}
}
private suspend fun searchById(id: String): List<ValueSet> =
listOfNotNull(
safeGet(fhirEngine, ResourceType.ValueSet, id.removePrefix(URN_OID).removePrefix(URN_UUID))
as? ValueSet
)

private suspend fun safeGet(fhirEngine: FhirEngine, type: ResourceType, id: String): Resource? {
return try {
Expand All @@ -119,7 +119,7 @@ class FhirEngineTerminologyProvider(
}
}

fun resolveValueSet(valueSet: ValueSetInfo): ValueSet {
private suspend fun resolveValueSet(valueSet: ValueSetInfo): ValueSet {
if (valueSet.version != null ||
(valueSet.codeSystems != null && valueSet.codeSystems.isNotEmpty())
) {
Expand All @@ -146,7 +146,7 @@ class FhirEngineTerminologyProvider(
}
}

fun resolveValueSetId(valueSet: ValueSetInfo): String {
suspend fun resolveValueSetId(valueSet: ValueSetInfo): String {
return resolveValueSet(valueSet).idElement.idPart
}
}

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